Contacts of the strand formed by residues 28 - 36 (chain B) in PDB entry 4BC1


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with PRO 28 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  ARG*     4.3    15.5    -      -       +      +
     22B  LEU      3.7     5.6    -      -       -      +
     23B  LYS*     5.2     0.9    -      -       -      -
     27B  GLY*     1.3    84.7    -      -       -      +
     29B  VAL*     1.3    69.2    +      -       -      +
    104B  PRO*     4.7     0.7    -      -       -      +
    105B  TYR*     3.4    54.9    +      -       +      +
    140B  GLN*     4.0     8.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 29 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  ILE      3.5     0.5    -      -       -      +
     21B  ARG*     3.4     6.5    -      -       -      -
     22B  LEU*     2.9    48.9    +      -       +      +
     24B  ALA*     3.8    22.2    -      -       +      -
     28B  PRO*     1.3    79.8    -      -       -      +
     30B  SER*     1.3    62.4    +      -       -      +
     31B  ALA      3.8     0.2    +      -       -      -
    102B  TRP*     4.9     3.4    -      -       +      -
    103B  THR      3.2    22.4    -      -       -      +
    104B  PRO*     4.0     2.7    -      -       +      -
    105B  TYR*     4.0     7.6    -      -       -      +
    136B  ARG*     4.0    21.5    -      -       +      +
    139B  ALA*     3.7    25.1    -      -       +      -
    140B  GLN*     3.9     9.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 30 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  GLN*     4.1     6.9    +      -       -      +
      8B  LEU*     3.9    13.3    -      -       -      +
     20B  ILE      3.8     4.0    -      -       -      -
     29B  VAL*     1.3    72.4    -      -       -      +
     31B  ALA*     1.3    59.3    +      -       -      +
     32B  PHE*     4.2    14.3    -      -       -      -
    101B  VAL      4.2     0.2    -      -       -      +
    102B  TRP*     3.5     5.9    -      -       -      +
    103B  THR*     2.9    50.7    +      -       -      +
    104B  PRO      4.0     6.4    +      -       -      -
    105B  TYR*     3.2    27.8    -      -       -      +
    107B  ARG*     5.4     4.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 31 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  GLY*     3.2     5.7    -      -       -      -
     20B  ILE*     2.9    45.4    +      -       +      +
     22B  LEU*     3.6    31.2    -      -       +      -
     29B  VAL      4.9     0.4    -      -       -      +
     30B  SER*     1.3    74.2    -      -       -      +
     32B  PHE*     1.3    63.5    +      -       -      +
     33B  LEU*     3.8    14.6    -      -       +      -
    101B  VAL      3.6     4.3    -      -       -      -
    102B  TRP*     4.1     8.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 32 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  GLN      4.0    13.0    -      -       -      -
      8B  LEU*     3.3    25.4    -      -       +      -
     10B  VAL*     3.5    29.2    -      -       +      -
     17B  LEU*     4.7     9.9    -      -       +      -
     18B  ARG      4.5     2.7    -      -       -      -
     19B  GLY*     3.5    18.6    -      -       -      -
     30B  SER*     4.2    11.9    -      -       -      -
     31B  ALA*     1.3    76.9    -      -       -      +
     33B  LEU*     1.3    61.7    +      -       -      +
     34B  GLY      4.0     0.2    -      -       -      -
     35B  ILE*     3.7    25.1    -      -       +      +
     62B  ALA*     3.6     9.0    -      -       +      -
    100B  ASN*     3.3     4.5    -      -       -      -
    101B  VAL*     2.9    39.5    +      -       +      +
    103B  THR*     4.0    14.1    -      -       -      -
    107B  ARG*     5.7     1.3    -      -       -      -
    190B  PHE*     3.3    31.4    -      +       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 33 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20B  ILE*     4.7     4.3    -      -       +      -
     22B  LEU*     4.9     8.3    -      -       +      -
     31B  ALA*     3.8    26.5    -      -       +      -
     32B  PHE*     1.3    78.8    -      -       -      +
     34B  GLY*     1.3    60.6    +      -       -      +
     61B  ASP      4.6     0.9    -      -       -      +
     62B  ALA*     3.0    25.5    +      -       -      +
     63B  THR      4.1    15.7    -      -       -      +
     64B  THR*     2.7    32.2    -      -       -      +
     65B  PHE*     3.9    35.4    -      -       +      +
    100B  ASN*     3.5    13.2    -      -       +      +
    101B  VAL      4.5     0.7    -      -       -      +
    102B  TRP*     4.1    24.5    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 34 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  LEU*     1.3    74.8    -      -       -      +
     35B  ILE*     1.3    67.2    +      -       -      +
     36B  PRO*     3.2    10.0    -      -       -      +
     60B  LEU*     4.4     5.9    -      -       -      +
     61B  ASP      5.0     1.6    -      -       -      +
     62B  ALA*     5.1     4.0    -      -       -      -
     64B  THR      4.3     0.9    -      -       -      -
     66B  GLN*     3.9    19.7    +      -       -      +
     98B  TYR*     3.4    22.7    -      -       -      -
     99B  LEU      3.0    12.1    +      -       -      -
    100B  ASN*     3.1     6.2    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 35 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  LEU*     3.7    36.6    -      -       +      -
     32B  PHE*     3.7    27.6    -      -       +      +
     34B  GLY*     1.3    75.1    -      -       -      +
     36B  PRO*     1.3    78.7    -      -       +      +
     37B  PHE      3.5     0.3    +      -       -      -
     56B  TRP*     5.1     4.9    -      -       +      -
     60B  LEU*     5.0     0.7    -      -       -      -
     62B  ALA*     4.6     2.6    -      -       +      +
     98B  TYR*     3.3     0.3    -      -       -      -
     99B  LEU*     2.9    37.0    +      -       +      +
    101B  VAL*     3.7    20.0    -      -       +      -
    182B  TRP*     3.5    43.7    -      -       +      +
    190B  PHE*     4.0     2.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 36 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17B  LEU*     4.9     0.2    -      -       +      -
     34B  GLY      3.2     8.5    -      -       -      +
     35B  ILE*     1.3    96.1    -      -       +      +
     37B  PHE*     1.3    60.1    +      -       -      +
     38B  ALA      3.7     3.1    -      -       -      +
     53B  LYS*     4.0    39.8    -      -       +      +
     56B  TRP*     4.7     7.5    -      -       +      -
     60B  LEU*     3.7    34.8    -      -       +      -
     97B  LEU      3.8     1.3    -      -       -      +
     98B  TYR*     3.3    29.2    -      -       +      -
    182B  TRP*     4.4     4.5    +      -       -      -
----------------------------------------------------------
 Back to top of page


A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il